You can change the font used for input and output cells in all notebooks to your preferred one, such as Courier, by evaluating the following:

    CurrentValue[$FrontEnd, {StyleHints, "CodeFont"}] = "Courier"    

This will undo these changes.

   CurrentValue[$FrontEnd, {StyleHints, "CodeFont"}] = Inherited     

Note that the fonts used in mathematics typesetting are the supplied MathFonts. This setting cannot be changed.

To alter the styling of a given font, edit the input or output cell style in a stylesheet.

Here we demonstrate the procedure for input cells. The procedure for output cells is the same.

  1. From the menu bar, select FormatEdit Stylesheet. A blank stylesheet opens.
  2. Under Choose a style, select the Input cell style and make sure the Input cell bracket is highlighted.

    Edit Stylesheet window - Input

  3. Use the Format menu selection to edit the characteristics (FormatFace or Background Color, for example). Here we change the font face to italic:

    showing Format >  Face to change part of style sheet.

  4. Click the upper-right button, Install Stylesheet. An install dialog appears. Enter the stylesheet name and select who the users will be. Click OK to confirm.
  5. Install System Item - style sheet, this user

Now this stylesheet is available under FormatStylesheet.

You may wish to make this stylesheet the default one for your Mathematica.